@jbrowse/product-core 5.0.0-beta.10 → 5.0.0-beta.13

package/esm/ui/aboutTestUtils.d.ts

@@ -23,12 +23,47 @@ export declare const TestTrackConf: import("@jbrowse/core/configuration/configur
         } & {
             defaultValue: unknown;
         };
+        readonly baiLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly metadata: {
         type: "frozen";
     } & {
         defaultValue: unknown;
     };
+    readonly textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly searchLabel: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly indexingAttributes: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly feature: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly subfeatures: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly depth: {
+            type: "maybeNumber";
+        };
+        readonly maxDepth: {
+            type: "maybeNumber";
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly config: {
             type: "frozen";
@@ -69,12 +104,47 @@ export declare function makeTrackConf(snapshot: SnapshotIn<typeof TestTrackConf>
         } & {
             defaultValue: unknown;
         };
+        readonly baiLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly metadata: {
         type: "frozen";
     } & {
         defaultValue: unknown;
     };
+    readonly textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly searchLabel: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly indexingAttributes: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly feature: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly subfeatures: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly depth: {
+            type: "maybeNumber";
+        };
+        readonly maxDepth: {
+            type: "maybeNumber";
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly config: {
             type: "frozen";
@@ -114,12 +184,47 @@ export declare function makeTrackConf(snapshot: SnapshotIn<typeof TestTrackConf>
         } & {
             defaultValue: unknown;
         };
+        readonly baiLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly metadata: {
         type: "frozen";
     } & {
         defaultValue: unknown;
     };
+    readonly textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly searchLabel: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly indexingAttributes: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly feature: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly subfeatures: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly depth: {
+            type: "maybeNumber";
+        };
+        readonly maxDepth: {
+            type: "maybeNumber";
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly config: {
             type: "frozen";

package/esm/ui/aboutTestUtils.js

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-import { ConfigurationSchema, FormatAboutConfigSchemaFactory, } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, } from '@jbrowse/core/configuration';
 // a real PluginManager provides the jexl instance a callback slot evaluates with
 export const aboutTestPluginManager = new PluginManager([]).createPluggableElements();
 aboutTestPluginManager.configure();
@@ -14,8 +14,22 @@ export const TestTrackConf = ConfigurationSchema('TestTrack', {
             type: 'fileLocation',
             defaultValue: { uri: '', locationType: 'UriLocation' },
         },
+        baiLocation: {
+            type: 'fileLocation',
+            defaultValue: { uri: '', locationType: 'UriLocation' },
+            advanced: true,
+        },
     }),
     metadata: { type: 'frozen', defaultValue: {} },
+    textSearching: ConfigurationSchema('TestTextSearching', {
+        searchLabel: { type: 'string', defaultValue: '' },
+        indexingAttributes: {
+            type: 'stringArray',
+            defaultValue: [],
+            advanced: true,
+        },
+    }),
+    formatDetails: FormatDetailsConfigSchemaFactory(),
     formatAbout: FormatAboutConfigSchemaFactory(),
 }, { explicitIdentifier: 'trackId' });
 export function makeTrackConf(snapshot) {

package/esm/ui/descriptionHtml.d.ts

@@ -1,20 +1,42 @@
+export type TrackDescription = {
+    url: string;
+} | {
+    html: string;
+};
 /**
- * The URL of a track's prose description page in its `metadata`, as a UCSC
- * track hub supplies it, and undefined for anything that is not an http(s) url
- * — the value reaches `openLocation` and an anchor's href, so a `javascript:`
- * or `file://` one does not become one here.
+ * A track's prose description in its `metadata`, as UCSC trackDb supplies it:
+ * a link to a page to fetch, or the page itself.
  *
  * Four spellings: `UCSCTrackHubConnection` spreads the trackDb stanza across
  * `metadata`, the bulk converter behind genomes.jbrowse.org nests it under
  * `metadata.ucsc` (~50,700 configs at permanent URLs), and the stanza key is
  * `html` for a track and `htmlPath` for an assembly. Both producers write an
- * escaped anchor rather than a bare url, so the href comes back through a parse
- * rather than a regex.
+ * escaped anchor for a hub's page, so the href comes back through a parse. The
+ * converter writes golden-path assemblies' pages inline, and only under `ucsc`
+ * is markup read as a page, so a track's own `html` column stays a column.
+ *
+ * A url is http(s) only: it reaches `openLocation` and an anchor's href.
+ * `path` names the key read, which the metadata card leaves out.
+ */
+export declare function findTrackDescription(metadata: unknown): {
+    description: {
+        url: string;
+        html?: undefined;
+    } | {
+        url?: undefined;
+        html: string;
+    };
+    path: string[];
+} | undefined;
+export declare function getTrackDescription(metadata: unknown): TrackDescription | undefined;
+/**
+ * `metadata` without the key its description came from, since the Description
+ * card shows that one.
  */
-export declare function getDescriptionHtmlUrl(metadata: unknown): string | undefined;
+export declare function omitTrackDescription(metadata: Record<string, unknown>): Record<string, unknown>;
 /**
- * A fetched description page as markup for `SanitizedHTML`: links and images
- * resolved against the page they came from rather than the JBrowse origin, and
+ * A description page as markup for `SanitizedHTML`: links and images resolved
+ * against the page they came from rather than the JBrowse origin, and
  * `<form>` dropped, which the sanitizer keeps and which in a document off a
  * third-party origin is a credential prompt wearing the app's own chrome.
  *

package/esm/ui/descriptionHtml.js

@@ -1,33 +1,86 @@
 function isRecord(value) {
     return typeof value === 'object' && value !== null;
 }
-function descriptionUrl(value) {
-    const href = new DOMParser()
-        .parseFromString(value, 'text/html')
-        .querySelector('a[href]')
-        ?.getAttribute('href');
-    const candidate = typeof href === 'string' ? href : value.trim();
-    return /^https?:\/\//i.test(candidate) ? candidate : undefined;
+function isHttpUrl(value) {
+    return /^https?:\/\//i.test(value);
 }
 /**
- * The URL of a track's prose description page in its `metadata`, as a UCSC
- * track hub supplies it, and undefined for anything that is not an http(s) url
- * — the value reaches `openLocation` and an anchor's href, so a `javascript:`
- * or `file://` one does not become one here.
+ * Where UCSC trackDb text sits when the golden-path assemblies the UCSC
+ * Genome Browser serves itself carry it inline: their `html` holds the page,
+ * written to render inside `hgTrackUi`, so its relative links (`hgTables`,
+ * `/goldenPath/help/…`) resolve against that.
+ */
+const UCSC_TRACK_PAGE = 'https://genome.ucsc.edu/cgi-bin/hgTrackUi';
+function parseDescription(value, inline) {
+    const body = new DOMParser().parseFromString(value, 'text/html').body;
+    const [first] = body.children;
+    if (!first) {
+        const text = value.trim();
+        return isHttpUrl(text) ? { url: text } : undefined;
+    }
+    const loneAnchor = body.children.length === 1 &&
+        first.matches('a[href]') &&
+        body.textContent.trim() === first.textContent.trim();
+    if (loneAnchor) {
+        const href = first.getAttribute('href') ?? '';
+        return isHttpUrl(href) ? { url: href } : undefined;
+    }
+    return inline
+        ? { html: rebaseDescriptionHtml(value, UCSC_TRACK_PAGE) }
+        : undefined;
+}
+/**
+ * A track's prose description in its `metadata`, as UCSC trackDb supplies it:
+ * a link to a page to fetch, or the page itself.
  *
  * Four spellings: `UCSCTrackHubConnection` spreads the trackDb stanza across
  * `metadata`, the bulk converter behind genomes.jbrowse.org nests it under
  * `metadata.ucsc` (~50,700 configs at permanent URLs), and the stanza key is
  * `html` for a track and `htmlPath` for an assembly. Both producers write an
- * escaped anchor rather than a bare url, so the href comes back through a parse
- * rather than a regex.
+ * escaped anchor for a hub's page, so the href comes back through a parse. The
+ * converter writes golden-path assemblies' pages inline, and only under `ucsc`
+ * is markup read as a page, so a track's own `html` column stays a column.
+ *
+ * A url is http(s) only: it reaches `openLocation` and an anchor's href.
+ * `path` names the key read, which the metadata card leaves out.
  */
-export function getDescriptionHtmlUrl(metadata) {
-    return [metadata, isRecord(metadata) ? metadata.ucsc : undefined]
-        .flatMap(record => (isRecord(record) ? [record.html, record.htmlPath] : []))
-        .filter(candidate => typeof candidate === 'string')
-        .map(candidate => descriptionUrl(candidate))
-        .find(url => url !== undefined);
+export function findTrackDescription(metadata) {
+    const ucsc = isRecord(metadata) ? metadata.ucsc : undefined;
+    const places = [
+        { record: metadata, prefix: [], inline: false },
+        { record: ucsc, prefix: ['ucsc'], inline: true },
+    ];
+    for (const { record, prefix, inline } of places) {
+        for (const key of ['html', 'htmlPath']) {
+            const value = isRecord(record) ? record[key] : undefined;
+            const description = typeof value === 'string' ? parseDescription(value, inline) : undefined;
+            if (description) {
+                return { description, path: [...prefix, key] };
+            }
+        }
+    }
+    return undefined;
+}
+export function getTrackDescription(metadata) {
+    return findTrackDescription(metadata)?.description;
+}
+/**
+ * `metadata` without the key its description came from, since the Description
+ * card shows that one.
+ */
+export function omitTrackDescription(metadata) {
+    const path = findTrackDescription(metadata)?.path;
+    if (!path) {
+        return metadata;
+    }
+    const [key = '', nestedKey] = path;
+    const nested = metadata[key];
+    return nestedKey !== undefined && isRecord(nested)
+        ? { ...metadata, [key]: without(nested, nestedKey) }
+        : without(metadata, key);
+}
+function without(record, key) {
+    return Object.fromEntries(Object.entries(record).filter(([k]) => k !== key));
 }
 function absolute(value, baseUrl) {
     try {
@@ -38,8 +91,8 @@ function absolute(value, baseUrl) {
     }
 }
 /**
- * A fetched description page as markup for `SanitizedHTML`: links and images
- * resolved against the page they came from rather than the JBrowse origin, and
+ * A description page as markup for `SanitizedHTML`: links and images resolved
+ * against the page they came from rather than the JBrowse origin, and
  * `<form>` dropped, which the sanitizer keeps and which in a document off a
  * third-party origin is a credential prompt wearing the app's own chrome.
  *

package/esm/ui/preferencesReset.d.ts

@@ -6,9 +6,6 @@ export interface ResettablePreferencesSession {
     setThemeMode: (arg: 'light' | 'dark' | 'system') => void;
     stickyViewHeaders: boolean;
     setStickyViewHeaders: (sticky: boolean) => void;
-    effectiveUseWorkspaces: boolean;
-    defaultUseWorkspaces: boolean;
-    resetUseWorkspaces: () => void;
     clearPreferenceOverrides: () => void;
     clearPreferenceOverride: (key: string) => void;
     getPreferenceChanges: () => TrackConfigChange[];

package/esm/ui/preferencesReset.js

@@ -26,19 +26,6 @@ const NON_MAP_PREFERENCES = [
             s.setStickyViewHeaders(true);
         },
     },
-    {
-        head: 'useWorkspaces',
-        change: s => s.effectiveUseWorkspaces === s.defaultUseWorkspaces
-            ? undefined
-            : {
-                path: ['useWorkspaces'],
-                from: s.defaultUseWorkspaces,
-                to: s.effectiveUseWorkspaces,
-            },
-        reset: s => {
-            s.resetUseWorkspaces();
-        },
-    },
 ];
 const NON_MAP_HEADS = new Set(NON_MAP_PREFERENCES.map(p => p.head));
 // Everything "Reset to defaults" reverts, as rows: the scalar overrides in the

package/esm/ui/util.d.ts

@@ -12,19 +12,18 @@ declare module '@jbrowse/core/PluginManager' {
         'Core-replaceAbout': ComponentSlot<AboutPanelProps>;
     }
 }
-/**
- * What a track's About dialog shows: the config with the session's and the
- * track's `formatAbout` callbacks merged over it, plus the resolved `hideUris`.
- * The two slots fold differently on purpose: `config` is a merge the track can
- * win key-by-key, `hideUris` an OR a track cannot turn back off.
- */
+/** About's two cards and `hideUris`, plus the raw `conf` Copy config copies. */
 export declare function getAboutDialogConfig({ config, session, }: {
     config: AnyConfigurationModel;
     session: AbstractSessionModel;
 }): {
+    conf: Record<string, unknown>;
     config: {
         [key: string]: unknown;
         metadata?: Record<string, unknown>;
     };
+    advanced: {
+        [k: string]: unknown;
+    };
     hideUris: boolean;
 };

package/esm/ui/util.js

@@ -1,19 +1,16 @@
-import { getConf, mergeFormatCallbacks, readConfObject, } from '@jbrowse/core/configuration';
+import { getConf, mergeFormatCallbacks, partitionAdvanced, readConfObject, } from '@jbrowse/core/configuration';
 // #endregion
-/**
- * What a track's About dialog shows: the config with the session's and the
- * track's `formatAbout` callbacks merged over it, plus the resolved `hideUris`.
- * The two slots fold differently on purpose: `config` is a merge the track can
- * win key-by-key, `hideUris` an OR a track cannot turn back off.
- */
+/** About's two cards and `hideUris`, plus the raw `conf` Copy config copies. */
 export function getAboutDialogConfig({ config, session, }) {
     const conf = readConfObject(config);
-    const shown = {
-        ...conf,
-        ...mergeFormatCallbacks(getConf(session, ['formatAbout', 'config'], { config: conf }), readConfObject(config, ['formatAbout', 'config'], { config: conf })),
-    };
+    const edits = mergeFormatCallbacks(getConf(session, ['formatAbout', 'config'], { config: conf }), readConfObject(config, ['formatAbout', 'config'], { config: conf }));
+    const split = partitionAdvanced(config, conf);
+    const shown = { ...split.rest, ...edits };
+    const advanced = Object.fromEntries(Object.entries(split.advanced).filter(([key]) => !(key in edits)));
     return {
+        conf,
         config: shown,
+        advanced,
         hideUris: Boolean(getConf(session, ['formatAbout', 'hideUris']) ||
             readConfObject(config, ['formatAbout', 'hideUris'])),
     };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.13",
   "type": "module",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
@@ -28,13 +28,13 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.6.1",
+    "@jbrowse/mobx-state-tree": "^6.7.0",
     "@mui/icons-material": "^9.4.0",
     "@mui/material": "^9.4.0",
-    "mobx": "^7.0.5",
+    "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
-    "@jbrowse/core": "^5.0.0-beta.10",
-    "@jbrowse/render-core": "^5.0.0-beta.10"
+    "@jbrowse/render-core": "^5.0.0-beta.13",
+    "@jbrowse/core": "^5.0.0-beta.13"
   },
   "peerDependencies": {
     "react": ">=19.0.0",